Scfd1 MGI Mouse Gene Detail - MGI:1924233 - Sec1 family domain containing 1

Symbol

Scfd1
Name

Sec1 family domain containing 1
Synonyms

3110021P21Rik, RA410, STXBP1L2

Feature Type

protein coding gene
IDs

MGI:1924233
NCBI Gene: 76983
Alliance

gene page
Transcription Start Sites

3 TSS

Sequence Map

Chr12:51424296-51496887 bp, + strand
From NCBI annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 12, 22.11 cM, cytoband C1
Mapping Data

2 experiments

SNPs within 2kb

2315 from dbSNP Build 142
Strain Annotations

18

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_1924233	protein coding gene	Chr12:51424293-51496887 (+)
129S1/SvImJ	MGP_129S1SvImJ_G0019723	protein coding gene	Chr12:50163602-50243355 (+)
A/J	MGP_AJ_G0019685	protein coding gene	Chr12:48401255-48474175 (+)
AKR/J	MGP_AKRJ_G0019656	protein coding gene	Chr12:49841984-49922203 (+)
BALB/cJ	MGP_BALBcJ_G0019663	protein coding gene	Chr12:48681718-48753702 (+)
C3H/HeJ	MGP_C3HHeJ_G0019466	protein coding gene	Chr12:49954751-50029108 (+)
C57BL/6NJ	MGP_C57BL6NJ_G0020111	protein coding gene	Chr12:51732871-51810089 (+)
CAROLI/EiJ	MGP_CAROLIEiJ_G0017734	protein coding gene	Chr12:46812283-46879198 (+)
CAST/EiJ	MGP_CASTEiJ_G0019019	protein coding gene	Chr12:44982453-45057574 (+)
CBA/J	MGP_CBAJ_G0019438	protein coding gene	Chr12:53502007-53573953 (+)
DBA/2J	MGP_DBA2J_G0019552	protein coding gene	Chr12:48258355-48331823 (+)
FVB/NJ	MGP_FVBNJ_G0019541	protein coding gene	Chr12:47708819-47782000 (+)
LP/J	MGP_LPJ_G0019624	protein coding gene	Chr12:50199086-50280083 (+)
NOD/ShiLtJ	MGP_NODShiLtJ_G0019577	protein coding gene	Chr12:55133490-55208706 (+)
NZO/HlLtJ	MGP_NZOHlLtJ_G0020149	protein coding gene	Chr12:49339807-49412915 (+)
PWK/PhJ	MGP_PWKPhJ_G0018786	protein coding gene	Chr12:42822251-42902401 (+)
SPRET/EiJ	MGP_SPRETEiJ_G0018580	protein coding gene	Chr12:43929292-44004188 (+)
WSB/EiJ	MGP_WSBEiJ_G0019070	protein coding gene	Chr12:49823586-49900975 (+)

Human Ortholog

SCFD1, sec1 family domain containing 1

Vertebrate Orthologs

3

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

SCFD1, sec1 family domain containing 1
Synonyms

C14orf163, RA410, SLY1, SLY1P, STXBP1L2
Links

HGNC:20726

NCBI Gene ID: 23256

neXtProt AC: NX_Q8WVM8

UniProt: Q8WVM8
Chr Location

14q12; chr14:30622254-30737694 (+) GRCh38

MGI Vertebrate Homology

Scfd1 stringent orthology
1 human;1 mouse;1 rat;1 zebrafish
HCOP

vertebrate homology predictions: SCFD1
Protein SuperFamily

VPS45_Sec1
Gene Tree

Scfd1

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Phenotype Summary

9 phenotypes from 1 allele in 1 genetic background
1 images
9 phenotype references

Phenotype Overview

Blue squares indicate phenotypes directly attributed to mutations/alleles of this gene.

adipose tissue	behavior/neurological	cardiovascular system	cellular	craniofacial	digestive/alimentary system	embryo	endocrine/exocrine glands	growth/size/body	hearing/vestibular/ear	hematopoietic system	homeostasis/metabolism	integument	immune system	limbs/digits/tail	liver/biliary system	mortality/aging	muscle	nervous system	pigmentation	renal/urinary system	reproductive system	respiratory system	skeleton	taste/olfaction	neoplasm	vision/eye

Click cells to view annotations.

All Mutations and Alleles

9
Chemically induced (other)

1
Endonuclease-mediated

1
Gene trapped

5
Targeted

2
Genomic Mutations

1 involving Scfd1
Incidental Mutations

Mutagenetix , APF , CvDC
Find Mice (IMSR)

34 strains or lines available
Comparison Matrix

Gene Expression + Phenotype

Mice homozygous for a knock-out allele show complete embryonic lethality prior to organogenesis. In vitro, some blastocysts fail to hatch from the zona pellucida and do not form outgrowths while others do hatch but form outgrowths with no inner cell mass and dispersed trophectoderm.

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All GO Annotations

29
GO References

7

Molecular Function

carbohydrate derivative binding	cytoskeletal protein binding	DNA binding	enzyme regulator	hydrolase	ligase	lipid binding	oxidoreductase	RNA binding	signaling receptor activity	signaling receptor binding	transcription	transferase	transporter

Biological Process

carbohydrate derivative metabolism	cell differentiation	cell population proliferation	cellular component organization	DNA-templated transcription	establishment of localization	homeostatic process	immune system process	lipid metabolic process	programmed cell death	protein metabolic process	response to stimulus	signaling	system development

Cellular Component

cell projection	cytoplasmic vesicle	cytoskeleton	cytosol	endoplasmic reticulum	endosome	extracellular region	Golgi apparatus	mitochondrion	membraneless organelle	nucleus	organelle envelope	organelle lumen	plasma membrane	protein-containing complex	synapse	vacuole

Click cells to view annotations.

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Expression Overview

GXD's primary emphasis is on endogenous gene expression during development. Click on grid cells to view annotations.

Blue cells = expressed in wild-type.
Gray triangles = other expression annotations only
(e.g. absence of expression or data from mutants).

early conceptus	embryo ectoderm	embryo endoderm	embryo mesoderm	embryo mesenchyme	extraembryonic component	alimentary system	auditory system	branchial arches	cardiovascular system	connective tissue	endocrine system	exocrine system	hemolymphoid system	integumental system	limbs	liver and biliary system	musculoskeletal system	nervous system	olfactory system	reproductive system	respiratory system	urinary system	visual system

Click cells to view annotations.

Assay Results

714
Tissues

1
cDNA Data

81
Literature Summary

1

Images

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

Other Mouse Links

Allen Institute

GEO

Expression Atlas
Other Vertebrate Links

Xenbase scfd1

ZFIN scfd1

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All Sequences

51
RefSeq

6
UniProt

3
CCDS

CCDS36439.1, CCDS88336.1

Ensembl

ENSMUSG00000020952 (Evidence)
NCBI Gene

76983

			Length	Strain/Species	Flank
genomic	76983	NCBI Gene Model \| MGI Sequence Detail	72592	C57BL/6J	± kb
transcript	NR_157117	RefSeq \| MGI Sequence Detail	3170	C57BL/6
polypeptide	Q8BRF7	UniProt \| EBI \| MGI Sequence Detail	639	Not Applicable

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UniProt

3 Sequences
Protein Ontology

PR:000014500 Sec1 family domain-containing protein 1

(term hierarchy)
InterPro Domains

IPR043154 Sec1-like, domain 1

IPR027482 Sec1-like, domain 2

IPR043127 Sec1-like, domain 3a

IPR001619 Sec1-like protein

IPR036045 Sec1-like superfamily
GlyGen

Q8BRF7 1 site, 1 N-linked glycan (1 site)

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All nucleic 81

cDNA 81

Microarray probesets 4

Summaries

All 37

Developmental Gene Expression 1

Gene Ontology 7

Phenotypes 9
Earliest

J:65060 Kawai J, et al., Functional annotation of a full-length mouse cDNA collection. Nature. 2001 Feb 8;409(6821):685-90
Latest

J:345621 Adams DJ, et al., Genetic determinants of micronucleus formation in vivo. Nature. 2024 Mar;627(8002):130-136

TSS for Scfd1:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr113414	Chr12:51424329-51424340 (+)	39 bp
Tssr113415	Chr12:51424343-51424370 (+)	61 bp
Tssr113416	Chr12:51425069-51425077 (+)	777 bp

Contributing Projects: Mouse Genome Database (MGD), Gene Expression Database (GXD), Mouse Models of Human Cancer database (MMHCdb) (formerly Mouse Tumor Biology (MTB)), Gene Ontology (GO)
Citing These Resources Funding Information Warranty Disclaimer, Privacy Notice, Licensing, & Copyright Send questions and comments to User Support.	last database update 11/19/2024 MGI 6.24